Of course, many types of file access can be worked around. For example, configuration information can be placed in LDAP, JNDI, a database, or even properties files delivered inside your JAR files that get loaded as a resource through the classloader. In those circumstances where accessing files is a requirement, then other solutions include loading the file through the servlet container, having it sent to the EJB tier via messaging, downloading the file from a webserver through a socket connection and so on.
These are all workarounds for the programming restriction but at the end of the day I think you have to be pragmatic.
The sort of pragmatism we see is lots of use of JSP's, and not a lot of use of EJB. This sort of thing explains a lot of that. Of course, I use Smalltalk Server pages, so the entire problem is avoided....